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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG

Basic information

species Zea mays
transcript GRMZM2G113202_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
gtaatgcacttttctttacctaaagttgtcat-atatattaaattccatatagttacttctgacattat-catatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
|||||| ||||   |||  |  | | |||||| |||| |||| |  || || ||| ||  || ||| |  || | ||||||| ||||||||||||||||||||| ||||| ||||||||||||||| | || |||||||||||||| ||||||||||||||||| ||||||
gtaatgtacttccatttgac--atgctgtcatcatattttaattggcaaatggtttctcatgtcataacacaaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 12
--------------------------------------gta-atgcacttttcttta-cctaaagttgtcatatatattaaattccatata--gttacttctgacat-tatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                      ||   || | || ||  || ||| |   | |   || | ||||| |   |     |||   |  |     | | ||   |||||| |||||||||||| |||||||| || |||||||| ||||| || || || ||||| |||||||||||||| || ||| | || || |||
gtatgttatattatatgacagatcttttatatgtgtgtgtgtgtgtatttatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgcggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 12
------------------------------------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctgacat---tatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                           | ||  |  |  |  | | | |   |||   |||| | ||||    |     ||||  ||  ||   | | ||   |||||| |||||||||||| ||||||||||| |||||||| ||||| || || |||||||| || ||||||||||| || ||| | || || |||
gtatgtttatattaaactttatctacatctttctatatatttatgatttatctcaccat-cttcatcctgtttgatat-taaaatattttggctctactgatgctatgcattttatgcctgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTTAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
------------------------------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                     || |     ||| | |  | |   |  || | | |  ||  || | | || | |       |||| | ||   |||||| |||||||||||||||||||||||| |||||||| ||||| || || |||||||| |||||||||||||| || ||| | || || |||
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcatt-ttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 14
-------------------------------------gtaatgcacttttctttacctaaagttgtcatatatattaaat-tccatatagttacttctgacat-tatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                      |  || |  |  || | | ||   |  | |  | | | |||| |       |||   | ||     | | ||   |||||| |||||||||||| ||||||||||| |||||||| ||||| || || || ||||| |||||||||||||| || ||| | || || |||
gtatgttatattatatggcagatcttttatatgcgtttttgtgtatatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgtggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 14
---------------------------------------------------gtaat--gcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctgacattatcatat---ttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                                   |  ||  |||| || | |   ||   |||    | | ||  ||  |  || | |||   |     | ||  |||    |||||||| || |||||||| |||||||| || |||||||| ||||| || ||||||||||| ||||| |||||| | || ||||||||||| |||
gtatgctggtttttagtctccctttgcgttttactgcatgaacttacataagctatctgcacattacatcttctgt-gttacattttgtaccaatgttaatttggtttgctgaataaatactatacatgttgcagAAAAATAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTCAACCGTCATCTCTTCAAGCTTGAGCAGGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------------------------------------------------------------------------------------------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttact-tctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                                                                                                            |||  ||||| | |  | |   |  | || ||| |    |   ||  | || || |  ||| ||      | ||||||| || || || || |||||||| || |||||||| ||||| || ||||||||||| || || |||||| | || ||||| |||||||||
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatt-tcttgatttatgt---gtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 13
------------------------gtaatgcacttttctttacctaaagttgtcat-atatattaaattccatatagttacttctgacattatc-atatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                        ||||   | ||||| || ||   | |   |||  |      || |  ||| |  | | | | ||||  ||  | ||| ||||  || || ||||| ||||||||||| |||||||| ||||| ||||||||||| || || || |||||||| || ||| | |||||||||
gtatgatattatttagtttctgctgtaaataatttttcattccccccattccccattgtccccctaaatttataaatattcatgttacatattctgtttttccagAGAAATAGCTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGGTTGCAGCAGCACTTTAACCGTCATTTATTCAAGTTAGAGCAAGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
----------gtaatgcacttttctttacctaaagt---tgtcatata-tattaaattccatatagttac----ttctgacattatcata---tttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
           |  |    ||||    | |||   |   ||   |||| ||||  | |   ||   | ||     ||     |||||      ||||||||  || ||||| || ||  | || || || ||||| ||||| ||| |||||||||||||||| |||||  | ||||||||||||||||| 
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------------------gtaat-gcacttttctttacctaaagttgtcatatat--attaaa----ttccatatagt-tacttctgacatta---tcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                               |||| |     |  | ||   |||| | | || | |  ||| |      | | ||| || ||  |    ||||    || |  |||||||||||||||||||| ||||| ||||| || ||||| || ||||||||||| |||||||||||||| ||| ||||||||||||||||||||
gtgaaatcttctcatacactagaatgagattgtaagcagtttattattaattgtttcctgatctagtcaaagctttgatttctggattgatggctcttcttatggtctagcttaagcatttccctcctgattgcagAAGAACAGTTTTGAGCAGTTATGCATAAACTATGCAAACGAAAGGTTGCAACAACATTTCAATCGCCATCTGTTTAAGCTTGAGCAAGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S17_368V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                          ||  | ||   || |      ||| || |||| || |||  |     |    ||| |  |  |  | ||||  |||||||| ||||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||||||||| ||||| |||||||||||||||
ttattgtaggaacctgatacaagtaggttttacaaaattttcacgtcaaatttttcatctacattggaagttgtt---ttaatctt--cgctttcatgattgcagAAAAACAGTTTTGAGCAGTTGTGTATTAACTACGCAAACGAAAGATTGCAACAACATTTCAATCGTCACTTGTTCAAGCTTGAGCAAGAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctga----cattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                    | |   ||| |  |  | |  || |  ||  |  ||   |   || |  ||  |    |     | |||  |  |||||||| ||||||||||| || || || || |||||||| |||||||||||||| |||||||||||||||||| |||| |||||||||||||||
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32930639|gb|CF035451.1|CF035451
EST:     CTGGGAGATCTATCAGTATTCTTGATATCTATGGCTNTGAGTCATTTGAT                         AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAG
genomic: CTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatgcact ... atatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAG
EST: gi|211452365|gb|FL406340.1|FL406340
EST:     CTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGAT                         AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAG
genomic: CTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatgcact ... atatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 687

GTGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatgcact ... atatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 456

GTGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatgcact ... atatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 353

GTGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatgcact ... atatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 712

GTGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTCGAACTGGGAGATCTATCAGTATTCTTGATATCTATGGCTTTGAATCATTTGATgtaatgcact ... atatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtcatatatattaaattccatatagttacttctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
                                ttctgac  putative branch site (score: 712)
      atatatattaaattcc  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA